Since I am working on PloneSoftwareCenter to make it PyPI-compatible, I
have worked on distutils side to make the register and upload
command more friendly when an egg has to be registered to several
servers.

The problem with the actual .pypirc file is that it won't let you
define many username/password for many servers: it is dedicated for one
server. In the meantime, you can specify in a command line option which
server you want to deal with:
$ python setup.py register -r http://my.server/pypi

But this will take the username/password in .pypirc. So if your
username differs from one server to another, it won't work.

The patch is ready, and comes with new unit tests register and
upload commands didn't have yet. The new .pypirc format was shaped
with the help and feedback of catalog-sig people, thanks to Martin v.
Loewis and Fred Drake and others. I am going to submit it for inclusion
today. If it is accepted and integrated we will be able to deal with our
eggs like this:
$ python setup.py register sdist upload # goes to PyPI

The next step is to provide a patch for a permissive trove classifier
in PyPI. Then all PyPI-like servers will be able to provide the same
service for egg developers, no matter how they deal with classifiers.